We have reported that activated neutrophils utilize the myeloperoxidase-H2O2-chloride system to convert the amino acid L-tyrosine to p-hydroxyphenylacetaldehyde. We report here that this myeloperoxidase system also catalyzes the oxidation of other amino acids to aldehydes. A sensitive method has been developed to detect these aldehydes as pentafluorobenzyl-oxime (PFBO) derivatives by GC/NICI/MS. The reagent pentafluorobenzylhydroxylamine was used to prepare these derivatives. Two geometric isomers are obtained that are separable on GC analysis and exhibit distinguishable NICI mass spectra. Major fragment ions observed in these spectra include (M-HF)-. Loss of HF from the molecular anion may yield a ring intermediate, the subsequent decomposition of which yields other ions in the spectra. These include ions generated by elimination of NO or HCN. Proposed fragmentation pathways are supported by collisionally activated dissociation and tandem mass spectrometry, high resolution m ass spectrometry, and studies of deuterium-labeled analogs.